Please note that this is a draft schedule and will inevitably change to some extent.

1   |   1/19   |  An Introduction to Biofabrication


In Class

Homework

2  |   1/26  |  Transcription & Translation: understanding in vivo, simulating in silico

 

In Class

  • class canceled due to snow
  • a portion of the class content has been pushed into homework

Homework

 

3  |   2/2  |  Digestion  & Ligation: simulating in silico, performing in vitro

In Class

  • review readings
  • review quiz
  • Introduction to Alba, a Grasshopper plugin for Synthetic Biology
    • Transcription and Translation
    • Digestion and Ligation
  • Lab Project part I: Digestion and Ligation

Homework

  • DO: Mini-lab sessions –
    •  transform cells FRIDAY 3:30-6:00
      • insert constructed plasmid into E. Coli
      • allow the cells to recover in rich media
      • plate the cells on agar plates with Ampicillin
      • place in incubator overnight
    • check on growth SATURDAY afternoon ~30 min
      • examine plates for colonies
      • use UV light to look for fluorescent protein expression
      • if growth looks good move plates to 4c refrigerator
      • if growth is not strong or evident at all, give them another day in the incubator
    • culture cells in liquid media MONDAY 3:00-4:00
      • examine colonies for expression of fluorescent protein
      • select a good looking colony
      • inoculate LB media with colony
      • incubate overnight in shaker
      • (optional) help make agar plates for next class
  • READ: Synthetic Biology Primer Ch5 part 2, Logic
  • PLAN: make stencils
    • Here is a template if you’d like to make your stencil on the laser cutter.
      Petri_Stencil_Template_Trotec
    • There is autoclavable plastic film in the laser booth, taped to the wall
    • you can also cut your stencil by hand out of aluminum foil

 

4  |   2/9  |  Programming and Making with Proteins

In Class

Homework

  • GO: Ryan Hammond Talk on Open Source Gendercodes
    • Tuesday 2/9 after class at 5:30pm.
    • Lazarus Center auditorium
    • OSG website
  • DO: Repeat the exercise we did in class with GFP for your RFP or YFP gene
    • see the Alba page for reference
    • put the promoter sequence and the protein R+E+T sequence on their respective plasmids
    • visualize these complete DNA sequences
    • highlight the parts within the plasmid
    • digest the parts with the enzymes used in the lab protocol
    • ligate the parts together
    • visualize the assembled sequence
    • highlight the four constituent parts and the antibiotic resistance
    • transcribe the gene based on RBS and terminator sequences
    • translate that RNA into an amino acid sequence
    • visualize the AA sequence
    • look up the AA sequence online
    • download the .PDB file for your protein
    • visualize the protein in Alba
    • export an image of:
      • your GH file (Grasshopper -> File -> Export Hi-Res Image…)
      • the DNA and AA visualizations (Top View, zoomed out,  Rhino -> File -> Print)
      • the protein visualization (Perspective view,  Rhino -> File -> Print)
    • Upload the three images and the .gh file here:
  • PLAN: prep files for bioprinting- create 2D geometry in Rhino or Grasshopper to draw with the printer
5  |   2/16  |  Bioprinting

In Class

  • Discuss readings from Synthetic Aesthetics
  • Xylinus
  • 2D bioprinting

Homework

 

 

 

6  |   2/23  |  Biomachines

In Class

  • lecture from visiting scientist, Dr.Rebecca Schulman, Assistant professor, Chemical and biomolecular engineering and computer science, JHU
  • groups session: imagining nanotech applications
  • catching up
    The snow days have pushed us into an intensive run through multiple complex technologies. Lets take a moment to catch up, talk about the readings from the semester, and contextualize all of this new knowledge.

    • discuss Synthetic Biology Primer ch 7 “Applications of Designed Biological Systems”
    • discuss Synthetic Aesthetics readings ch 1-2
    • brief lecture – bioprinting overview

Homework

  • read Synthetic Aesthetic essay by Daisy Ginsberg
  • independent research and exploration
  • begin sketching ideas for project
7  |   3/1  |  Scaling up

In Class

  • discuss reading
  • bioprinting
  • field trip

Homework

  • prepare a 5-10 minute talk with slides that answer the following questions:
    1. What is the most interesting thing you’ve learned in class so far?
    2. What is a project from another artist/designer/researcher that uses biology in a way you find inspiring?
    3. What is an approach to manufacturing (loosely interpreted) that you find compelling?
    4. Describe an intersection of biology and another discipline that you find exciting.
    5. What do you want to continue to explore?

 

8  |   3/8  |  Establishing Group Projects

In Class

  • presentations
  • discussion
  • determine groups and topics

Homework

  • begin working on projects

 

9  |   3/15  | Spring Break

 

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